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Jones K, Keddy C, Jenkins C, Nicholson K, Shinde U, Davare MA. Novel insight into mechanisms of ROS1 catalytic activation via loss of the extracellular domain. Sci Rep 2024; 14:22191. [PMID: 39333184 PMCID: PMC11437283 DOI: 10.1038/s41598-024-71687-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/30/2024] [Indexed: 09/29/2024] Open
Abstract
The ROS1 receptor tyrosine kinase (RTK) possesses the largest extracellular amino-terminal domain (ECD) among the human RTK family, yet the mechanisms regulating its activation are not fully understood. While chimeric ROS1 fusion proteins, resulting from chromosomal rearrangements, are well-known oncogenic drivers, their activation mechanisms also remain underexplored. To elucidate the role of the ROS1 ECD in catalytic regulation, we engineered a series of amino-terminal deletion mutants. Our functional studies compared the full-length ROS1 receptor, the CD74-ROS1 oncogenic fusion, and ECD-deleted ROS1 constructs, identifying the ECD regions that inhibit ROS1 tyrosine kinase activity. Notably, we found that deletion of the ROS1 ECD alone significantly increases constitutive catalytic activation and neoplastic transformation in the absence of an amino-terminal fusion partner, challenging the presumed necessity for a dimerization domain in the activation mechanism of kinase fusions in cancer. Our data suggest that inter-genic deletions resulting in the loss of the ECD may be underappreciated oncogenic drivers in cancer. Furthermore, our studies demonstrate that RNASE7 is not a ligand for the ROS1 receptor as previously reported, confirming that ROS1 remains an orphan receptor. Thus, the discovery of a ROS1 ligand remains an important future priority. These findings highlight the potential for disease-associated somatic aberrations or splice variants that modify the ROS1 ECD to promote constitutive receptor activation, warranting further investigation.
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Affiliation(s)
- Kristen Jones
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Clare Keddy
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Chelsea Jenkins
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Katelyn Nicholson
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Ujwal Shinde
- Department of Chemical Physiology and Biochemistry, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Monika A Davare
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA.
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2
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Myall NJ, Das M. ROS1-rearranged non-small cell lung cancer: Understanding biology and optimizing management in the era of new approvals. Curr Probl Cancer 2024; 53:101133. [PMID: 39260124 DOI: 10.1016/j.currproblcancer.2024.101133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/10/2024] [Accepted: 06/26/2024] [Indexed: 09/13/2024]
Abstract
Rearrangements involving the ROS1 gene are infrequent in non-small cell lung cancer (NSCLC) but represent an important targetable driver alteration. Occurring most commonly in patients with adenocarcinoma who have a light or never smoking history, ROS1 rearrangements can be identified by either fluorescence in-situ hybridization (FISH) or next-generation sequencing techniques. Multiple tyrosine kinase inhibitors (TKIs) are now available for the effective treatment of ROS1-rearranged NSCLC in the metastatic setting including crizotinib, entrectinib, and repotrectinib as first-line therapy options. In addition, newer targeted therapies with increased selectivity for ROS1 over other targets are also emerging. As treatment of the disease continues to evolve, understanding the clinical course of patients with ROS1-rearranged NSCLC as well as the data supporting the latest therapy options is key to timely, effective, and longitudinal care.
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Affiliation(s)
- Nathaniel J Myall
- Division of Oncology, Department of Medicine, Stanford Cancer Center, Stanford CA, United States
| | - Millie Das
- Division of Oncology, Department of Medicine, Stanford Cancer Center, Stanford CA, United States; Department of Medicine, VA Palo Alto Health Care System, 3801 Miranda Ave. (111ONC), Palo Alto CA 94304, United States.
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3
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Tóth LJ, Mokánszki A, Méhes G. The rapidly changing field of predictive biomarkers of non-small cell lung cancer. Pathol Oncol Res 2024; 30:1611733. [PMID: 38953007 PMCID: PMC11215025 DOI: 10.3389/pore.2024.1611733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Lung cancer is a leading cause of cancer-related death worldwide in both men and women, however mortality in the US and EU are recently declining in parallel with the gradual cut of smoking prevalence. Consequently, the relative frequency of adenocarcinoma increased while that of squamous and small cell carcinomas declined. During the last two decades a plethora of targeted drug therapies have appeared for the treatment of metastasizing non-small cell lung carcinomas (NSCLC). Personalized oncology aims to precisely match patients to treatments with the highest potential of success. Extensive research is done to introduce biomarkers which can predict the effectiveness of a specific targeted therapeutic approach. The EGFR signaling pathway includes several sufficient targets for the treatment of human cancers including NSCLC. Lung adenocarcinoma may harbor both activating and resistance mutations of the EGFR gene, and further, mutations of KRAS and BRAF oncogenes. Less frequent but targetable genetic alterations include ALK, ROS1, RET gene rearrangements, and various alterations of MET proto-oncogene. In addition, the importance of anti-tumor immunity and of tumor microenvironment has become evident recently. Accumulation of mutations generally trigger tumor specific immune defense, but immune protection may be upregulated as an aggressive feature. The blockade of immune checkpoints results in potential reactivation of tumor cell killing and induces significant tumor regression in various tumor types, such as lung carcinoma. Therapeutic responses to anti PD1-PD-L1 treatment may correlate with the expression of PD-L1 by tumor cells. Due to the wide range of diagnostic and predictive features in lung cancer a plenty of tests are required from a single small biopsy or cytology specimen, which is challenged by major issues of sample quantity and quality. Thus, the efficacy of biomarker testing should be warranted by standardized policy and optimal material usage. In this review we aim to discuss major targeted therapy-related biomarkers in NSCLC and testing possibilities comprehensively.
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Affiliation(s)
- László József Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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4
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Ou SHI, Hagopian GG, Zhang SS, Nagasaka M. Comprehensive Review of ROS1 Tyrosine Kinase Inhibitors-Classified by Structural Designs and Mutation Spectrum (Solvent Front Mutation [G2032R] and Central β-Sheet 6 [Cβ6] Mutation [L2086F]). J Thorac Oncol 2024; 19:706-718. [PMID: 38070596 DOI: 10.1016/j.jtho.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
Abstract
Despite ROS1 fusion-positive NSCLC accounting for approximately 1% to 2% of NSCLC, there is a long list of ROS1 tyrosine kinase inhibitors (TKIs) being developed in addition to three approved ROS1 TKIs, crizotinib, entrectinib and repotrectinib. Here, we categorized ROS1 TKIs by their structures (cyclic versus noncyclic) and inhibitory abilities (active against solvent front mutation G2032R or central β-sheet #6 [Cβ6] mutation L2086F) and summarized their reported clinical activity in order to provide a dashboard on how to use these ROS1 TKIs in various clinical situations. In addition, the less known Cβ6 mutation ROS1 L2086F confer resistances to next-generation ROS1 TKIs (repotrectinib, taletrectinib, and potentially NVL-520) that can be overcome by cabozantinib as documented in published patient reports and potentially by certain L-shaped type I ROS1 TKIs including ceritinib and gilteritinib, which is approved as a FLT3 inhibitor for relapsed refractory FLT3+ acute myeloid leukemia but have published preclinical activites against ROS1 (and ALK). Future clinical trials should investigate cabozantinib and gilteritinib to repurpose them as ROS1 TKIs that can target ROS1 L2086F Cβ6 mutation.
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Affiliation(s)
- Sai-Hong Ignatius Ou
- Department of Medicine, University of California Irvine School of Medicine, Orange, California; Chao Family Comprehensive Cancer Center, Orange, California.
| | - Garo G Hagopian
- Department of Medicine, University of California Irvine School of Medicine, Orange, California
| | - Shannon S Zhang
- Department of Medicine, University of California Irvine School of Medicine, Orange, California
| | - Misako Nagasaka
- Department of Medicine, University of California Irvine School of Medicine, Orange, California; Chao Family Comprehensive Cancer Center, Orange, California
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5
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Lee B, Chern A, Fu AY, Zhang A, Sha MY. A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer. Diagnostics (Basel) 2024; 14:488. [PMID: 38472960 DOI: 10.3390/diagnostics14050488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Lung cancer is often triggered by genetic alterations that result in the expression of oncogenic tyrosine kinases. Specifically, ALK, RET, and ROS1 chimeric receptor tyrosine kinases are observed in approximately 5-7%, 1-2%, and 1-2% of NSCLC patients, respectively. The presence of these fusion genes determines the response to tyrosine kinase inhibitors. Thus, accurate detection of these gene fusions is essential in cancer research and precision oncology. To address this need, we have developed a multiplexed RT-qPCR assay using xeno nucleic acid (XNA) molecular clamping technology to detect lung cancer fusions. This assay can quantitatively detect thirteen ALK, seven ROS1, and seven RET gene fusions in FFPE samples. The sensitivity of the assay was established at a limit of detection of 50 copies of the synthetic template. Our assay has successfully identified all fusion transcripts using 50 ng of RNA from both reference FFPE samples and cell lines. After validation, a total of 77 lung cancer patient FFPE samples were tested, demonstrating the effectiveness of the XNA-based fusion gene assay with clinical samples. Importantly, this assay is adaptable to highly degraded RNA samples with low input amounts. Future steps involve expanding the testing to include a broader range of clinical samples as well as cell-free RNAs to further validate its applicability and reliability.
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Affiliation(s)
- Bongyong Lee
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Andrew Chern
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Andrew Y Fu
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Aiguo Zhang
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Michael Y Sha
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
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6
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Al-Ghabkari A, Huang B, Park M. Aberrant MET Receptor Tyrosine Kinase Signaling in Glioblastoma: Targeted Therapy and Future Directions. Cells 2024; 13:218. [PMID: 38334610 PMCID: PMC10854665 DOI: 10.3390/cells13030218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Brain tumors represent a heterogeneous group of neoplasms characterized by a high degree of aggressiveness and a poor prognosis. Despite recent therapeutic advances, the treatment of brain tumors, including glioblastoma (GBM), an aggressive primary brain tumor associated with poor prognosis and resistance to therapy, remains a significant challenge. Receptor tyrosine kinases (RTKs) are critical during development and in adulthood. Dysregulation of RTKs through activating mutations and gene amplification contributes to many human cancers and provides attractive therapeutic targets for treatment. Under physiological conditions, the Met RTK, the hepatocyte growth factor/scatter factor (HGF/SF) receptor, promotes fundamental signaling cascades that modulate epithelial-to-mesenchymal transition (EMT) involved in tissue repair and embryogenesis. In cancer, increased Met activity promotes tumor growth and metastasis by providing signals for proliferation, survival, and migration/invasion. Recent clinical genomic studies have unveiled multiple mechanisms by which MET is genetically altered in GBM, including focal amplification, chromosomal rearrangements generating gene fusions, and a splicing variant mutation (exon 14 skipping, METex14del). Notably, MET overexpression contributes to chemotherapy resistance in GBM by promoting the survival of cancer stem-like cells. This is linked to distinctive Met-induced pathways, such as the upregulation of DNA repair mechanisms, which can protect tumor cells from the cytotoxic effects of chemotherapy. The development of MET-targeted therapies represents a major step forward in the treatment of brain tumours. Preclinical studies have shown that MET-targeted therapies (monoclonal antibodies or small molecule inhibitors) can suppress growth and invasion, enhancing the efficacy of conventional therapies. Early-phase clinical trials have demonstrated promising results with MET-targeted therapies in improving overall survival for patients with recurrent GBM. However, challenges remain, including the need for patient stratification, the optimization of treatment regimens, and the identification of mechanisms of resistance. This review aims to highlight the current understanding of mechanisms underlying MET dysregulation in GBM. In addition, it will focus on the ongoing preclinical and clinical assessment of therapies targeting MET dysregulation in GBM.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
| | - Bruce Huang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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7
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Georgescu MM. Translation into Clinical Practice of the G1-G7 Molecular Subgroup Classification of Glioblastoma: Comprehensive Demographic and Molecular Pathway Profiling. Cancers (Basel) 2024; 16:361. [PMID: 38254850 PMCID: PMC10814912 DOI: 10.3390/cancers16020361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Glioblastoma is the most frequent and malignant primary neoplasm of the central nervous system. In a recent breakthrough study on a prospective Discovery cohort, I proposed the first all-inclusive molecular classification of glioblastoma into seven subgroups, G1-G7, based on MAPK pathway activation. New data from a WHO-grade-4 diffuse glioma prospective Validation cohort offers, in this study, an integrated demographic-molecular analysis of a 213-patient Combined cohort. Despite cohort differences in the median age and molecular subgroup distribution, all the prospectively-acquired cases from the Validation cohort mapped into one of the G1-G7 subgroups defined in the Discovery cohort. A younger age of onset, higher tumor mutation burden and expanded G1/EGFR-mutant and G3/NF1 glioblastoma subgroups characterized the glioblastomas from African American/Black relative to Caucasian/White patients. The three largest molecular subgroups were G1/EGFR, G3/NF1 and G7/Other. The fourth largest subgroup, G6/Multi-RTK, was detailed by describing a novel gene fusion ST7-MET, rare PTPRZ1-MET, LMNA-NTRK1 and GOPC-ROS1 fusions and their overexpression mechanisms in glioblastoma. The correlations between the MAPK pathway G1-G7 subgroups and the PI3-kinase/PTEN, TERT, cell cycle G1 phase and p53 pathways defined characteristic subgroup pathway profiles amenable to personalized targeted therapy. This analysis validated the first all-inclusive molecular classification of glioblastoma, showed significant demographic and molecular differences between subgroups, and provided the first ethnic molecular comparison of glioblastoma.
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Sourty B, Basset L, Michalak S, Colin E, Zidane-Marinnes M, Delion M, de Carli E, Rousseau A. [Tyrosine kinase receptor gene fusion: A series of four cases of infantile-type hemispheric glioma]. Ann Pathol 2023; 43:462-474. [PMID: 37635016 DOI: 10.1016/j.annpat.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023]
Abstract
INTRODUCTION Infant-type hemispheric gliomas belong to pediatric-type diffuse high-grade gliomas according to the 2021 WHO classification of central nervous system tumors. They are characterized by tyrosine kinase gene rearrangements (NTRK1/2/3, ALK, ROS1, MET). The aim of the study was to describe the clinical, histopathologic, and molecular characteristics of such tumors, and to provide a review of the literature. PATIENTS AND METHODS This retrospective series comprises four cases of infant-type hemispheric glioma diagnosed at Angers University Hospital between 2020 and 2022. The diagnosis was suspected based on morphology and immunohistochemistry and was confirmed by molecular biology techniques. RESULTS The most common clinical sign was raised intracranial pressure. Imaging showed a large cerebral hemispheric tumor with contrast enhancement. Microscopic examination revealed diffuse astrocytoma with high-grade features, sometimes with neuronal or pseudo-ependymal differentiation. Identification of a gene fusion involving a tyrosine kinase gene allowed to make a definitive diagnosis of infant-type hemispheric glioma. DISCUSSION AND CONCLUSION Infant-type hemispheric gliomas are rare and present as large cerebral hemispheric tumors in very young children. Searching for a tyrosine kinase gene fusion should be systematic when dealing with a high-grade glioma in an infant. Importantly, these gene fusions are therapeutic targets. The impact of targeted therapies on patient survival should be evaluated in future prospective studies.
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Affiliation(s)
- Baptiste Sourty
- Département de pathologie, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France.
| | - Laëtitia Basset
- Département de pathologie, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France; Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, 49000 Angers, France
| | - Sophie Michalak
- Département de pathologie, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France
| | - Estelle Colin
- Service de génétique médicale, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France
| | | | - Matthieu Delion
- Service de neurochirurgie, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France
| | - Emilie de Carli
- Unité hémato-onco-immunologie pédiatrique, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France
| | - Audrey Rousseau
- Département de pathologie, CHU d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France; Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, 49000 Angers, France
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9
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Meredith DM, Cooley LD, Dubuc A, Morrissette J, Sussman RT, Nasrallah MP, Rathbun P, Yap KL, Wadhwani N, Bao L, Wolff DJ, Ida C, Sukhanova M, Horbinski C, Jennings LJ, Farooqi M, Gener M, Ginn K, Kam KL, Sasaki K, Kanagal-Shamanna R, Alexandrescu S, Brat D, Lu X. ROS1 Alterations as a Potential Driver of Gliomas in Infant, Pediatric, and Adult Patients. Mod Pathol 2023; 36:100294. [PMID: 37532182 DOI: 10.1016/j.modpat.2023.100294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Gliomas harboring oncogenic ROS1 alterations are uncommon and primarily described in infants. Our goal was to characterize the clinicopathological features and molecular signatures of the full spectrum of ROS1 fusion-positive gliomas across all age groups. Through a retrospective multi-institutional collaboration, we report a collection of unpublished ROS1 fusion gliomas along with the characterization and meta-analysis of new and published cases. A cohort of 32 new and 58 published cases was divided into the following 3 age groups: 19 infants, 40 pediatric patients, and 31 adults with gliomas. Tumors in infants and adults showed uniformly high-grade morphology; however, tumors in pediatric patients exhibited diverse histologic features. The GOPC::ROS1 fusion was prevalent (61/79, 77%) across all age groups, and 10 other partner genes were identified. Adult tumors showed recurrent genomic alterations characteristic of IDH wild-type glioblastoma, including the +7/-10/CDKN2A deletion; amplification of CDK4, MDM2, and PDGFRA genes; and mutations involving TERTp, TP53, PIK3R1, PIK3CA, PTEN, and NF1 genes. Infant tumors showed few genomic alterations, whereas pediatric tumors showed moderate genomic complexity. The outcomes were significantly poorer in adult patients. Although not statistically significant, tumors in infant and pediatric patients with high-grade histology and in hemispheric locations appeared more aggressive than tumors with lower grade histology or those in nonhemispheric locations. In conclusion, this study is the largest to date to characterize the clinicopathological and molecular signatures of ROS1 fusion-positive gliomas from infant, pediatric, and adult patients. We conclude that ROS1 likely acts as a driver in infant and pediatric gliomas and as a driver or codriver in adult gliomas. Integrated comprehensive clinical testing might be helpful in identifying such patients for possible targeted therapy.
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Affiliation(s)
- David M Meredith
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Linda D Cooley
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, University of Missouri School of Medicine, Kansas City, Missouri
| | - Adrian Dubuc
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jennifer Morrissette
- Pathology and Laboratory Medicine, Division of Precision and Computational Diagnostics, Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robyn T Sussman
- Pathology and Laboratory Medicine, Division of Precision and Computational Diagnostics, Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - MacLean P Nasrallah
- Pathology and Laboratory Medicine, Division of Neuropathology, Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pamela Rathbun
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Nitin Wadhwani
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Liming Bao
- Department of Pathology School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Cristiane Ida
- Department of Pathology, School of Medicine, Mayo clinic, Scottsdale, Arizona
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, Lurie Cancer Center, Chicago, Illinois
| | - Craig Horbinski
- Department of Pathology, Northwestern University Feinberg School of Medicine, Lurie Cancer Center, Chicago, Illinois
| | - Lawrence J Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Lurie Cancer Center, Chicago, Illinois
| | - Midhat Farooqi
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, University of Missouri School of Medicine, Kansas City, Missouri
| | - Melissa Gener
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, University of Missouri School of Medicine, Kansas City, Missouri
| | - Kevin Ginn
- Division of Hematology/Oncology/Blood and Marrow Transplant, Children's Mercy Kansas City & School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Kwok Ling Kam
- Department of Pathology, Beaumont Hospital, Royal Oak, Michigan
| | - Koji Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Lurie Cancer Center, Chicago, Illinois
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Lurie Cancer Center, Chicago, Illinois.
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10
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Kurimoto M, Rockenbach Y, Kato A, Natsume A. Prediction of Tumor Development and Urine-Based Liquid Biopsy for Molecule-Targeted Therapy of Gliomas. Genes (Basel) 2023; 14:1201. [PMID: 37372381 DOI: 10.3390/genes14061201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The timing of the acquisition of tumor-specific gene mutations and the systems by which these gene mutations are acquired during tumorigenesis were clarified. Advances in our understanding of tumorigenesis are being made every day, and therapies targeting fundamental genetic alterations have great potential for cancer treatment. Moreover, our research team successfully estimated tumor progression using mathematical modeling and attempted early diagnosis of brain tumors. We developed a nanodevice that enables urinary genetic diagnosis in a simple and noninvasive manner. Mainly on the basis of our research and experience, this review article presents novel therapies being developed for central nervous system cancers and six molecules, which upon mutation cause tumorigenesis and tumor progression. Further understanding of the genetic characteristics of brain tumors will lead to the development of precise drugs and improve individual treatment outcomes.
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Affiliation(s)
- Michihiro Kurimoto
- Department of Neurosurgery, Aichi Children's Health and Medical Center, Obu 464-8710, Japan
| | - Yumi Rockenbach
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Akira Kato
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Natsume
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
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11
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Zhang HL, Kong Q. Current landscape and future prospects of RET and ROS1 targets. Pharm Pat Anal 2023; 12:113-126. [PMID: 37671904 DOI: 10.4155/ppa-2023-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
RET and ROS1 are becoming key targets for targeted therapy. To show current landscape of ROS1 and RET targets, a patent analysis was performed. The present results indicated that inhibitor structures of ROS1 target demonstrated unique elements compared with inhibitor structures of RET or BRAF targets. Our study was the first time to uncover that a number of inhibitor structures of ROS1 target contained sulfur and boron elements. The inhibitors of RET target could be developed for treatment of various cancers, including lung cancer, thyroid cancer, and other solid tumor, while the inhibitors of ROS1 target are virtually developed for treatment of lung cancer. Our findings provide a new insight for drug discovery of ROS1 and RET target.
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Affiliation(s)
- Hai-Long Zhang
- Central International Intellectual Property (Baotou) Co., Ltd., Baotou, 014030, China
| | - Qian Kong
- Department of Chemistry, College of Science, Southern University of Science & Technology, Shenzhen, 518055, China
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12
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Machida H, Matsuo K, Tanaka M, Kitatani K, Takase A, Yokoyama K, Kajiwara H, Yasaka M, Ikeda M, Yoshida H, Hirasawa T, Mikami M. ROS1 as a possible prognostic biomarker of cervical adenocarcinoma: An exploratory analysis with next-generation sequencing. Gynecol Oncol 2023; 171:59-66. [PMID: 36804622 DOI: 10.1016/j.ygyno.2023.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023]
Abstract
OBJECTIVES Given the differences in clinical and biological characteristics between cervical adenocarcinoma and squamous cell carcinoma, this study aimed to conduct an exploratory analysis to examine the molecular characteristics of cervical adenocarcinoma in a Japanese population. METHODS This study explored the simultaneous testing of multiple mutations targeting cervical adenocarcinoma using next-generation sequencing (NGS). The following genes were analyzed: BCAR4, CD274, PDCD1LG2, KRAS, ARID1A, PTEN, ALK, EGFR, ROS1, BRAF, PIK3CA, EP300, EBXW7, SHCBP1, TGFBR2, SMAD4, ERBB2, ERBB3, and KLF5. Tumor tissue and blood samples were obtained at the time of primary treatment. The NGS-based molecular profiles obtained from Tokai University (49 specimens) were compared with the registered data in The Cancer Genome Atlas (TCGA) database (133 specimens). RESULTS The study cohort had higher rates of adenocarcinoma than the TCGA cohort (44.9% vs. 18.0%; P = 0.001). The adenocarcinomas in the study cohort had more alterations in ROS1, EGFR, EP300, SHCBP1, ALK, and PIK3CA than those in the TCGA cohort. Among them, ROS1 had the highest number of gene alterations (median, 7.00 ± 2.63). In the study cohort, patients with a high number of ROS1 alterations had a significantly higher recurrence rate (5-year recurrence rate, 48.8% vs. 14.6%; hazard ratio [HR], 4.32; 95% confidence interval [CI], 1.20-15.50; P = 0.014) and lower overall survival than those with low alterations (5-year survival rate, 70.7% vs. 93.1%; HR, 7.15; 95% CI, 1.08-58.22; P = 0.032). CONCLUSION The current exploratory analysis suggests that ROS1 gene alteration may be a prognostic biomarker in cervical adenocarcinoma in Japanese patients.
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Affiliation(s)
- Hiroko Machida
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Kanagawa, Japan.
| | - Koji Matsuo
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Masayuki Tanaka
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Kanae Kitatani
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Akinori Takase
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Keiko Yokoyama
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Hiroshi Kajiwara
- Department of Pathology, Tokai University School of Medicine, Kanagawa, Japan
| | - Miwa Yasaka
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Kanagawa, Japan
| | - Masae Ikeda
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Kanagawa, Japan
| | - Hiroshi Yoshida
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Kanagawa, Japan
| | - Takeshi Hirasawa
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Kanagawa, Japan
| | - Mikio Mikami
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Kanagawa, Japan
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13
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Male sterility in ROS1 receptor tyrosine kinase conditionally deleted in epididymal epithelial. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119413. [PMID: 36535370 DOI: 10.1016/j.bbamcr.2022.119413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
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14
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Li N, Chen Z, Huang M, Zhang D, Hu M, Jiao F, Quan M. Detection of ROS1 gene fusions using next-generation sequencing for patients with malignancy in China. Front Cell Dev Biol 2022; 10:1035033. [PMID: 36589752 PMCID: PMC9798300 DOI: 10.3389/fcell.2022.1035033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Objective: This study aimed to identify ROS1 fusion partners in Chinese patients with solid tumors. Methods: Next-generation sequencing (NGS) analysis was used to detect ROS1 rearrangement in 45,438 Chinese patients with solid tumors between 2015 and 2020, and the clinical characteristics and genetic features of gene fusion were evaluated. H&E staining of the excised tumor tissues was conducted. Samples with a tumor cell content ≥ 20% were included for subsequent DNA extraction and sequencing analysis. Results: A total of 92 patients with ROS1 rearrangements were identified using next-generation sequencing, and the most common histological type lung cancer. From the 92 ROS1 fusion cases, 24 ROS1 fusion partners had been identified, including 14 novel partners and 10 reported partners. Of these, CD74, EZR, SDC4, and TPM3 were the four most frequently occurring partners. Fourteen novel ROS1 fusion partners were detected in 16 patients, including DCBLD1-ROS1, FRK-ROS1, and VGLL2-ROS1. In many patients, the ROS1 breakpoint was located between exons 32 and 34. Conclusion: This study describes 14 novel ROS1 fusion partners based on the largest ROS1 fusion cohort, and the ROS1 breakpoint was mostly located between exons 32 and 34. Additionally, next-generation sequencing is an optional method for identifying novel ROS1 fusions.
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Affiliation(s)
- Ning Li
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiqin Chen
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mei Huang
- Department of Oncology, Yancheng Third People’s Hospital, Yancheng, China
| | - Ding Zhang
- The Medical Department, 3D Medicines Co., Ltd., Shanghai, China
| | - Mengna Hu
- The Medical Department, 3D Medicines Co., Ltd., Shanghai, China
| | - Feng Jiao
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Feng Jiao, ; Ming Quan,
| | - Ming Quan
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China,*Correspondence: Feng Jiao, ; Ming Quan,
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15
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Slocum CC, Park HJ, Baek I, Catalano J, Wells MT, Liechty B, Mathew S, Song W, Solomon JP, Pisapia DJ. Towards a single-assay approach: a combined DNA/RNA sequencing panel eliminates diagnostic redundancy and detects clinically-relevant fusions in neuropathology. Acta Neuropathol Commun 2022; 10:167. [PMCID: PMC9670552 DOI: 10.1186/s40478-022-01466-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
AbstractSince the introduction of integrated histological and molecular diagnoses by the 2016 World Health Organization (WHO) Classification of Tumors of the Nervous System, an increasing number of molecular markers have been found to have prognostic significance in infiltrating gliomas, many of which have now become incorporated as diagnostic criteria in the 2021 WHO Classification. This has increased the applicability of targeted-next generation sequencing in the diagnostic work-up of neuropathology specimens and in addition, raises the question of whether targeted sequencing can, in practice, reliably replace older, more traditional diagnostic methods such as immunohistochemistry and fluorescence in-situ hybridization. Here, we demonstrate that the Oncomine Cancer Gene Mutation Panel v2 assay targeted-next generation sequencing panel for solid tumors is not only superior to IHC in detecting mutation in IDH1/2 and TP53 but can also predict 1p/19q co-deletion with high sensitivity and specificity relative to fluorescence in-situ hybridization by looking at average copy number of genes sequenced on 1p, 1q, 19p, and 19q. Along with detecting the same molecular data obtained from older methods, targeted-next generation sequencing with an RNA sequencing component provides additional information regarding the presence of RNA based alterations that have diagnostic significance and possible therapeutic implications. From this work, we advocate for expanded use of targeted-next generation sequencing over more traditional methods for the detection of important molecular alterations as a part of the standard diagnostic work up for CNS neoplasms.
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16
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In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma. Sci Rep 2022; 12:14439. [PMID: 36002559 PMCID: PMC9402576 DOI: 10.1038/s41598-022-18608-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022] Open
Abstract
RNA-Sequencing (RNA-Seq) can identify gene fusions in tumors, but not all these fusions have functional consequences. Using multiple data bases, we have performed an in silico analysis of fusions detected by RNA-Seq in tumor samples from 139 newly diagnosed glioblastoma patients to identify in-frame fusions with predictable oncogenic potential. Among 61 samples with fusions, there were 103 different fusions, involving 167 different genes, including 20 known oncogenes or tumor suppressor genes (TSGs), 16 associated with cancer but not oncogenes or TSGs, and 32 not associated with cancer but previously shown to be involved in fusions in gliomas. After selecting in-frame fusions able to produce a protein product and running Oncofuse, we identified 30 fusions with predictable oncogenic potential and classified them into four non-overlapping categories: six previously described in cancer; six involving an oncogene or TSG; four predicted by Oncofuse to have oncogenic potential; and 14 other in-frame fusions. Only 24 patients harbored one or more of these 30 fusions, and only two fusions were present in more than one patient: FGFR3::TACC3 and EGFR::SEPTIN14. This in silico study provides a good starting point for the identification of gene fusions with functional consequences in the pathogenesis or treatment of glioblastoma.
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17
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Zhang L, Wang D, Han X, Guo X, Cao Y, Xia Y, Gao D. Novel read-through fusion transcript Bcl2l2-Pabpn1 in glioblastoma cells. J Cell Mol Med 2022; 26:4686-4697. [PMID: 35894779 PMCID: PMC9443946 DOI: 10.1111/jcmm.17481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/11/2022] [Accepted: 06/19/2022] [Indexed: 11/29/2022] Open
Abstract
Read‐through fusion transcripts have recently been identified as chimeric RNAs and have since been linked to tumour growth in some cases. Many fusion genes generated by chromosomal rearrangements have been described in glioblastoma. However, read‐through fusion transcripts between neighbouring genes in glioblastoma remain unexplored. We performed paired‐end RNA‐seq of rat C6 glioma cells and normal cells and discovered a read‐through fusion transcript Bcl2l2‐Pabpn1 in which exon 3 of Bcl‐2‐like protein 2 (Bcl2l2) fused to exon 2 of Polyadenylate‐binding protein 1 (Pabpn1). This fusion transcript was found in both human glioblastoma and normal cells. Unlike other fusions reported in glioblastoma, Bcl2l2‐Pabpn1 appeared to result from RNA processing rather than genomic rearrangement. Bcl2l2‐Pabpn1 fusion transcript encoded a fusion protein with BH4, BCL and RRM domains. Functionally, Bcl2l2‐Pabpn1 knockdown by targeting its fusion junction decreased its expression, and suppressed cell proliferation, migration and invasion in vitro. Mechanistically, Bcl2l2‐Pabpn1 blocked Bax activity and activated PI3K/AKT pathway to promote glioblastoma progression. Together, our work characterized a glioblastoma‐associated Bcl2l2‐Pabpn1 fusion transcript shared by humans and rats.
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Affiliation(s)
- Lin Zhang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China.,School of Nursing, Xuzhou Medical University, Xuzhou, China
| | - Dan Wang
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Xiao Han
- Nanjing Medical University, Nanjing, China
| | - Xiaoxiao Guo
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Yuanyuan Cao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Ying Xia
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Dianshuai Gao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
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18
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Yu ZQ, Wang M, Zhou W, Mao MX, Chen YY, Li N, Peng XC, Cai J, Cai ZQ. ROS1-positive non-small cell lung cancer (NSCLC): Biology, Diagnostics, Therapeutics and Resistance. J Drug Target 2022; 30:845-857. [PMID: 35658765 DOI: 10.1080/1061186x.2022.2085730] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ROS1 is a proto-oncogene encoding a receptor tyrosine protein kinase (RTK), homologous to the v - Ros sequence of University of Manchester tumours virus 2(UR2) sarcoma virus, whose ligands are still being investigated. ROS1 fusion genes have been identified in various types of tumours. As an oncoprotein, it promotes cell proliferation, activation and cell cycle progression by activating downstream signalling pathways, accelerating the development and progression of non-small cell lung cancer (NSCLC). Studies have demonstrated that ROS1 inhibitors are effective in patients with ROS1-positive NSCLC and are used for first-line clinical treatment. These small molecule inhibitors provide a rational therapeutic option for the treatment of ROS1-positive patients. Inevitably, ROS1 inhibitor resistance mutations occur, leading to tumours recurrence or progression. Here, we comprehensively review the identified biological properties and Differential subcellular localization of ROS1 fusion oncoprotein promotes tumours progression. We summarize recently completed and ongoing clinical trials of the classic and new ROS1 inhibitors. More importantly, we classify the complex evolving tumours cell resistance mechanisms. This review contributes to our understanding of the biological properties of ROS1 and current therapeutic advances and resistant tumours cells, and the future directions to develop ROS1 inhibitors with durable effects.
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Affiliation(s)
- Zhi-Qiong Yu
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Meng Wang
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Wen Zhou
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Meng-Xia Mao
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Yuan-Yuan Chen
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Na Li
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Xiao-Chun Peng
- Laboratory of Oncology, Center for Molecular Medicine.,Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Jun Cai
- Department of Oncology, First Affiliated Hospital of Yangtze University
| | - Zhi-Qiang Cai
- Department of Oncology, First Affiliated Hospital of Yangtze University
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19
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Li Z, Sun Q, Shi Y. Somatic structural variations in pediatric brain tumors. Minerva Pediatr (Torino) 2022; 74:358-364. [DOI: 10.23736/s2724-5276.17.04830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Roosen M, Odé Z, Bunt J, Kool M. The oncogenic fusion landscape in pediatric CNS neoplasms. Acta Neuropathol 2022; 143:427-451. [PMID: 35169893 PMCID: PMC8960661 DOI: 10.1007/s00401-022-02405-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 01/09/2023]
Abstract
Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.
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Affiliation(s)
- Mieke Roosen
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Zelda Odé
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Jens Bunt
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands.
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany.
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21
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Gendarme S, Bylicki O, Chouaid C, Guisier F. ROS-1 Fusions in Non-Small-Cell Lung Cancer: Evidence to Date. Curr Oncol 2022; 29:641-658. [PMID: 35200557 PMCID: PMC8870726 DOI: 10.3390/curroncol29020057] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
The ROS-1 gene plays a major role in the oncogenesis of numerous tumors. ROS-1 rearrangement is found in 0.9–2.6% of non-small-cell lung cancers (NSCLCs), mostly lung adenocarcinomas, with a significantly higher rate of women, non-smokers, and a tendency to a younger age. It has been demonstrated that ROS-1 is a true oncogenic driver, and tyrosine kinase inhibitors (TKIs) targeting ROS-1 can block tumor growth and provide clinical benefit for the patient. Since 2016, crizotinib has been the first-line reference therapy, with two-thirds of the patients’ tumors responding and progression-free survival lasting ~20 months. More recently developed are ROS-1-targeting TKIs that are active against resistance mechanisms appearing under crizotinib and have better brain penetration. This review summarizes current knowledge on ROS-1 rearrangement in NSCLCs, including the mechanisms responsible for ROS-1 oncogenicity, epidemiology of ROS-1-positive tumors, methods for detecting rearrangement, phenotypic, histological, and molecular characteristics, and their therapeutic management. Much of this work is devoted to resistance mechanisms and the development of promising new molecules.
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Affiliation(s)
- Sébastien Gendarme
- INSERM, IMRB (Clinical Epidemiology and Ageing Unit), University Paris Est Créteil, F-94010 Créteil, France;
- Pneumology Department, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, F-94010 Créteil, France
- Correspondence:
| | - Olivier Bylicki
- Respiratory Disease Unit, HIA Sainte-Anne, 2, Boulevard Saint-Anne, F-83000 Toulon, France;
| | - Christos Chouaid
- INSERM, IMRB (Clinical Epidemiology and Ageing Unit), University Paris Est Créteil, F-94010 Créteil, France;
- Pneumology Department, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, F-94010 Créteil, France
| | - Florian Guisier
- Department of Pneumology, Rouen University Hospital, 1 Rue de Germont, F-76000 Rouen, France;
- Clinical Investigation Center, Rouen University Hospital, CIC INSERM 1404, 1 Rue de Germont, F-76000 Rouen, France
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22
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Batra U, Nathany S, Sachdeva R, Sharma M, Amrith BP, Vaidya S. ROS1 in non-small-cell lung carcinoma: A narrative review. CANCER RESEARCH, STATISTICS, AND TREATMENT 2022. [DOI: 10.4103/crst.crst_322_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
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23
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Abstract
PURPOSE OF REVIEW Glioma represents of variety of brain malignancies, the majority of which confer a poor prognosis despite treatment. With the widespread use of next-generation sequencing, gene fusions are being found in greater numbers. Gene fusions in glioma represent an opportunity to deliver targeted therapies to those with limited options for treatment. RECENT FINDINGS Extensive studies on these gene fusions have shown that they can exhibit distinct phenotypes, such as PTPRZ1-MET fusions in secondary glioblastoma or FGFR3-TACC3 fusions in IDH wildtype gliomas. Responses have been observed with the use of targeted therapies but some have been short lived because of the development of treatment resistance. SUMMARY Increasing detection of gene fusions in glioma along with basket trials have helped define different fusion phenotypes and paved the way for targeted kinase inhibitor-based therapies. Targeting NTRK fusions has been the most successful fusion-guided therapy to date and evaluating all patients for these fusions may be warranted.
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Affiliation(s)
- Peter L Kim
- Yale Brain Tumor Center, Yale Cancer Center and Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
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24
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You G, Fan X, Hu H, Jiang T, Chen CC. Fusion Genes Altered in Adult Malignant Gliomas. Front Neurol 2021; 12:715206. [PMID: 34671307 PMCID: PMC8520976 DOI: 10.3389/fneur.2021.715206] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
Malignant gliomas are highly heterogeneous brain tumors in molecular genetic background. Despite the many recent advances in the understanding of this disease, patients with adult high-grade gliomas retain a notoriously poor prognosis. Fusions involving oncogenes have been reported in gliomas and may serve as novel therapeutic targets to date. Understanding the gene fusions and how they regulate oncogenesis and malignant progression will contribute to explore new approaches for personalized treatment. By now, studies on gene fusions in gliomas remain limited. However, some current clinical trials targeting fusion genes have presented exciting preliminary findings. The aim of this review is to summarize all the reported fusion genes in high-grade gliomas so far, discuss the characterization of some of the most popular gene fusions occurring in malignant gliomas, as well as their function in tumorigenesis, and the underlying clinical implication as therapeutic targets.
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Affiliation(s)
- Gan You
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurophysiology, Beijing Neurosurgical Institute, Beijing, China
| | - Xing Fan
- Department of Neurophysiology, Beijing Neurosurgical Institute, Beijing, China
| | - Huimin Hu
- Department of Molecular Pathology, Beijing Neurosurgical Institute, Beijing, China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Molecular Pathology, Beijing Neurosurgical Institute, Beijing, China
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, United States
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25
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Jarahian M, Marofi F, Maashi MS, Ghaebi M, Khezri A, Berger MR. Re-Expression of Poly/Oligo-Sialylated Adhesion Molecules on the Surface of Tumor Cells Disrupts Their Interaction with Immune-Effector Cells and Contributes to Pathophysiological Immune Escape. Cancers (Basel) 2021; 13:5203. [PMID: 34680351 PMCID: PMC8534074 DOI: 10.3390/cancers13205203] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022] Open
Abstract
Glycans linked to surface proteins are the most complex biological macromolecules that play an active role in various cellular mechanisms. This diversity is the basis of cell-cell interaction and communication, cell growth, cell migration, as well as co-stimulatory or inhibitory signaling. Our review describes the importance of neuraminic acid and its derivatives as recognition elements, which are located at the outermost positions of carbohydrate chains linked to specific glycoproteins or glycolipids. Tumor cells, especially from solid tumors, mask themselves by re-expression of hypersialylated neural cell adhesion molecule (NCAM), neuropilin-2 (NRP-2), or synaptic cell adhesion molecule 1 (SynCAM 1) in order to protect themselves against the cytotoxic attack of the also highly sialylated immune effector cells. More particularly, we focus on α-2,8-linked polysialic acid chains, which characterize carrier glycoproteins such as NCAM, NRP-2, or SynCam-1. This characteristic property correlates with an aggressive clinical phenotype and endows them with multiple roles in biological processes that underlie all steps of cancer progression, including regulation of cell-cell and/or cell-extracellular matrix interactions, as well as increased proliferation, migration, reduced apoptosis rate of tumor cells, angiogenesis, and metastasis. Specifically, re-expression of poly/oligo-sialylated adhesion molecules on the surface of tumor cells disrupts their interaction with immune-effector cells and contributes to pathophysiological immune escape. Further, sialylated glycoproteins induce immunoregulatory cytokines and growth factors through interactions with sialic acid-binding immunoglobulin-like lectins. We describe the processes, which modulate the interaction between sialylated carrier glycoproteins and their ligands, and illustrate that sialic acids could be targets of novel therapeutic strategies for treatment of cancer and immune diseases.
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Affiliation(s)
- Mostafa Jarahian
- German Cancer Research Center, Toxicology and Chemotherapy Unit Heidelberg, 69120 Heidelberg, Germany;
| | - Faroogh Marofi
- Department of Hematology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5165665931, Iran;
| | - Marwah Suliman Maashi
- Stem Cells and Regenerative Medicine Unit at King Fahad Medical Research Centre, Jeddah 11211, Saudi Arabia;
| | - Mahnaz Ghaebi
- Cancer Gene Therapy Research Center (CGRC), Zanjan University of Medical Sciences, Zanjan 4513956184, Iran;
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2418 Hamar, Norway;
| | - Martin R. Berger
- German Cancer Research Center, Toxicology and Chemotherapy Unit Heidelberg, 69120 Heidelberg, Germany;
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26
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Koustas E, Trifylli EM, Sarantis P, Papavassiliou AG, Karamouzis MV. Role of autophagy in cholangiocarcinoma: An autophagy-based treatment strategy. World J Gastrointest Oncol 2021; 13:1229-1243. [PMID: 34721764 PMCID: PMC8529918 DOI: 10.4251/wjgo.v13.i10.1229] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/28/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Cholangiocarcinomas (CCAs) are diverse biliary epithelial tumours involving the intrahepatic, perihilar and distal parts of the biliary tree. The three entirely variable entities have distinct epidemiology, molecular characteristics, prognosis and strategy for clinical management. However, many cholangiocarcinoma tumor-cells appear to be resistant to current chemotherapeutic agents. The role of autophagy and the therapeutic value of autophagy-based therapy are largely unknown in CCA. The multistep nature of autophagy offers a plethora of regulation points, which are prone to be deregulated and cause different human diseases, including cancer. However, it offers multiple targetable points for designing novel therapeutic strategies. Tumor cells have evolved to use autophagy as an adaptive mechanism for survival under stressful conditions such as energy imbalance and hypoxic region of tumors within the tumor microenvironment, but also to increase invasiveness and resistance to chemotherapy. The purpose of this review is to summarize the current knowledge regarding the interplay between autophagy and cholangiocarcinogenesis, together with some preclinical studies with agents that modulate autophagy in order to induce tumor cell death. Altogether, a combinatorial strategy, which comprises the current anti-cancer agents and autophagy modulators, would represent a positive CCA patient approach.
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Affiliation(s)
- Evangelos Koustas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Eleni-Myrto Trifylli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Panagiotis Sarantis
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Michalis V Karamouzis
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
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Azelby CM, Sakamoto MR, Bowles DW. ROS1 Targeted Therapies: Current Status. Curr Oncol Rep 2021; 23:94. [PMID: 34125313 DOI: 10.1007/s11912-021-01078-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW Molecular drivers are increasingly identified as therapeutic targets for non-small cell lung cancer (NSCLC). This review focuses on the role of ROS1 inhibitors in treating relapsed/metastatic ROS-1 altered (ROS1+) NSCLC. RECENT FINDINGS Four FDA-approved drugs have significant activity against ROS1+ NSCLC: crizotinib, ciritinib, lorlatinib, and entrectinib. Each drug yields an overall response rates exceeding 60% with ciritinib, lorlatinib, and entrectinib possessing intracranial activity. The drugs have manageable toxicity profiles. ROS1 alterations are rare molecular drivers of NSCLC that can be effectively treated with a variety of ROS1-targetd drugs. New agents are being identified that may treat resistance mutations.
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Affiliation(s)
- Christine M Azelby
- Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, AU, USA
| | - Mandy R Sakamoto
- Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, AU, USA
| | - Daniel W Bowles
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, 1665 Aurora Court, Colorado, AU, USA. .,Rocky Mountain Regional VA Medical Center, Aurora, CO, USA.
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Liu C, Zha Z, Zhou C, Chen Y, Xia W, Wang YN, Lee HH, Yin Y, Yan M, Chang CW, Chan LC, Qiu Y, Li H, Li CW, Hsu JM, Hsu JL, Wang SC, Ren N, Hung MC. Ribonuclease 7-driven activation of ROS1 is a potential therapeutic target in hepatocellular carcinoma. J Hepatol 2021; 74:907-918. [PMID: 33031845 PMCID: PMC7979498 DOI: 10.1016/j.jhep.2020.09.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS There are currently limited therapeutic options for hepatocellular carcinoma (HCC), particularly when it is diagnosed at advanced stages. Herein, we examined the pathophysiological role of ROS1 and assessed the utility of ROS1-targeted therapy for the treatment of HCC. METHODS Recombinant ribonucleases (RNases) were purified, and the ligand-receptor relationship between RNase7 and ROS1 was validated in HCC cell lines by Duolink, immunofluorescence, and immunoprecipitation assays. Potential interacting residues between ROS1 and RNase7 were predicted using a protein-protein docking approach. The oncogenic function of RNase7 was analyzed by cell proliferation, migration and invasion assays, and a xenograft mouse model. The efficacy of anti-ROS1 inhibitor treatment was evaluated in patient-derived xenograft (PDX) and orthotopic models. Two independent patient cohorts were analyzed to evaluate the pathological relevance of RNase7/ROS1. RESULTS RNase7 associated with ROS1's N3-P2 domain and promoted ROS1-mediated oncogenic transformation. Patients with HCC exhibited elevated plasma RNase7 levels compared with healthy individuals. High ROS1 and RNase7 expression were strongly associated with poor prognosis in patients with HCC. In both HCC PDX and orthotopic mouse models, ROS1 inhibitor treatment markedly suppressed RNase7-induced tumorigenesis, leading to decreased plasma RNase7 levels and tumor shrinkage in mice. CONCLUSIONS RNase7 serves as a high-affinity ligand for ROS1. Plasma RNase7 could be used as a biomarker to identify patients with HCC who may benefit from anti-ROS1 treatment. LAY SUMMARY Receptor tyrosine kinases are known to be involved in tumorigenesis and have been targeted therapeutically for a number of cancers, including hepatocellular carcinoma. ROS1 is the only such receptor with kinase activity whose ligand has not been identified. Herein, we show that RNase7 acts as a ligand to activate ROS1 signaling. This has important pathophysiological and therapeutic implications. Anti-ROS1 inhibitors could be used to treatment patients with hepatocellular carcinoma and high RNase7 levels.
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Affiliation(s)
- Chunxiao Liu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhengyu Zha
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chenhao Zhou
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Yeh Chen
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Weiya Xia
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heng-Huan Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yirui Yin
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Meisi Yan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Pathology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Chiung-Wen Chang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li-Chuan Chan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yufan Qiu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Third Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, China
| | - Hui Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Chia-Wei Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jung-Mao Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Jennifer L Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Ning Ren
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China.
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan.
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Goto K, Pissaloux D, Kauer F, Huriet V, Tirode F, de la Fouchardière A. GOPC-ROS1 mosaicism in agminated Spitz naevi: report of two cases. Virchows Arch 2021; 479:559-564. [PMID: 33733342 DOI: 10.1007/s00428-020-02992-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 02/02/2023]
Abstract
Spitz tumors are genetically associated with activating HRAS point mutations or fusions of either ALK, ROS1, NTRK1, NTRK3, RET, MET, MERTK, LCK, BRAF, MAP3K8, or MAP3K3. All these driver gene alterations are mutually exclusive. We report two cases of agminated Spitz naevi with a GOPC-ROS1 fusion. Both cases occurred on the lower limb of young adults. Since adolescence, pigmented or pink-colored papules have been periodically arising in a limited area of skin. In one case, an ill-defined hyperpigmented macule known since childhood was present in the background. Morphologically, at least five lesions were analyzed from each patient. In one case, all were predominantly junctional pigmented Spitz naevi, and in the other case, all were compound unpigmented Spitz naevi. No atypical features were present. RNA-sequencing revealed a GOPC-ROS1 gene translocation in both cases. Split signals of ROS1 gene in fluorescence in situ hybridization were observed not only in the nests of spitzoid melanocytes but also in the bland basal melanocytes surrounding the proliferations. These findings suggest the presence of a GOPC-ROS1 mosaicism in melanocytes with further emergence of agminated Spitz naevi potentially triggered by other genetic alterations. This expands the spectrum of genetic anomalies described in agminated Spitz naevi and our understanding of the mechanisms involved in their emergence.
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Affiliation(s)
- Keisuke Goto
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Tokyo, Japan.,Department of Pathology, Itabashi Central Clinical Laboratory, Tokyo, Japan.,Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Nagaizumi, Japan.,Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan.,Department of Dermatology, Hyogo Cancer Center, Akashi, Japan
| | - Daniel Pissaloux
- Department of Biopathology, Center Léon Bérard, 28, rue Laennec, 69008, Lyon, France.,Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | | | | | - Franck Tirode
- Department of Biopathology, Center Léon Bérard, 28, rue Laennec, 69008, Lyon, France.,Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Arnaud de la Fouchardière
- Department of Biopathology, Center Léon Bérard, 28, rue Laennec, 69008, Lyon, France. .,Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France.
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Drilon A, Jenkins C, Iyer S, Schoenfeld A, Keddy C, Davare MA. ROS1-dependent cancers - biology, diagnostics and therapeutics. Nat Rev Clin Oncol 2021; 18:35-55. [PMID: 32760015 PMCID: PMC8830365 DOI: 10.1038/s41571-020-0408-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 12/14/2022]
Abstract
The proto-oncogene ROS1 encodes a receptor tyrosine kinase with an unknown physiological role in humans. Somatic chromosomal fusions involving ROS1 produce chimeric oncoproteins that drive a diverse range of cancers in adult and paediatric patients. ROS1-directed tyrosine kinase inhibitors (TKIs) are therapeutically active against these cancers, although only early-generation multikinase inhibitors have been granted regulatory approval, specifically for the treatment of ROS1 fusion-positive non-small-cell lung cancers; histology-agnostic approvals have yet to be granted. Intrinsic or extrinsic mechanisms of resistance to ROS1 TKIs can emerge in patients. Potential factors that influence resistance acquisition include the subcellular localization of the particular ROS1 oncoprotein and the TKI properties such as the preferential kinase conformation engaged and the spectrum of targets beyond ROS1. Importantly, the polyclonal nature of resistance remains underexplored. Higher-affinity next-generation ROS1 TKIs developed to have improved intracranial activity and to mitigate ROS1-intrinsic resistance mechanisms have demonstrated clinical efficacy in these regards, thus highlighting the utility of sequential ROS1 TKI therapy. Selective ROS1 inhibitors have yet to be developed, and thus the specific adverse effects of ROS1 inhibition cannot be deconvoluted from the toxicity profiles of the available multikinase inhibitors. Herein, we discuss the non-malignant and malignant biology of ROS1, the diagnostic challenges that ROS1 fusions present and the strategies to target ROS1 fusion proteins in both treatment-naive and acquired-resistance settings.
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Affiliation(s)
- Alexander Drilon
- Early Drug Development and Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Chelsea Jenkins
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Sudarshan Iyer
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Adam Schoenfeld
- Early Drug Development and Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Clare Keddy
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Monika A Davare
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.
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Ah-Pine F, Casas D, Menei P, Boisselier B, Garcion E, Rousseau A. RNA-sequencing of IDH-wild-type glioblastoma with chromothripsis identifies novel gene fusions with potential oncogenic properties. Transl Oncol 2021; 14:100884. [PMID: 33074125 PMCID: PMC7569239 DOI: 10.1016/j.tranon.2020.100884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most frequent and most aggressive form of glioma. It is characterized by marked genomic instability, which suggests that chromothripsis (CT) might be involved in GBM initiation. Recently, CT has emerged as an alternative mechanism of cancer development, involving massive chromosome rearrangements in a one-step catastrophic event. The aim of the study was to detect CT in GBM and identify novel gene fusions in CT regions. One hundred and seventy IDH-wild-type GBM were screened for CT patterns using whole-genome single nucleotide polymorphism (SNP) arrays. RNA sequencing was performed in 52 GBM with CT features to identify gene fusions within CT regions. Forty tumors (40/52, 77%) harbored at least one gene fusion within CT regions. We identified 120 candidate gene fusions, 30 of which with potential oncogenic activities. We validated 11 gene fusions, which involved the most recurrent fusion partners (EGFR, SEPT14, VOPP1 and CPM), by RT-PCR and Sanger sequencing. The occurrence of CT points to underlying gene fusions in IDH-wild-type GBM. CT provides exciting new research avenues in this highly aggressive cancer.
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Key Words
- baf, b-allele frequency
- chr, chromosome
- cna, copy number alteration
- cns, central nervous system
- ct, chromothripsis
- fpkm, fragments per kilobase of exon per million fragments mapped
- gbm, glioblastoma multiform
- hd, homozygous deletion
- loh, loss of heterozygosity
- rna-seq, rna sequencing
- rt-pcr, reverse transcriptase – polymerase chain reaction
- snp, single nucleotide polymorphism
- who, world health organization
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Affiliation(s)
- Franck Ah-Pine
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, 4 rue Larrey, 49100 Angers, France
| | - Déborah Casas
- CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France.
| | - Philippe Menei
- Département de Neurochirurgie, CHU Angers, 4 rue Larrey, 49100 Angers, France.
| | - Blandine Boisselier
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, 4 rue Larrey, 49100 Angers, France; CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France
| | - Emmanuel Garcion
- CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France.
| | - Audrey Rousseau
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, 4 rue Larrey, 49100 Angers, France; CRCINA, INSERM, Université de Nantes, Université d'Angers, 4 rue Larrey, 49100 Angers, France.
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Abstract
ROS1-rearranged non-small cell lung cancer (NSCLC) makes up approximately 1% to 2% of all NSCLC, is oncogenically driven by a constitutively activated ROS1 kinase paired with certain fusion partners, and can be detected by several different assays. These patients are initially treated with tyrosine kinase inhibitors (TKIs), which target the activated ROS1 kinase. Eventually these tumors develop resistance to initial TKI treatment through secondary kinase mutations that block TKI binding or activation of bypass signaling pathways, which subvert ROS1 as the driver of the malignancy. Investigation of several TKIs that have shown efficacy in secondary resistant patients is underway.
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Zheng J, Cao H, Li Y, Rao C, Zhang T, Luo J, Lv D, Zhu Y, Zhou J, Zhou J. Effectiveness and prognostic factors of first-line crizotinib treatment in patients with ROS1-rearranged non-small cell lung cancer: A multicenter retrospective study. Lung Cancer 2020; 147:130-136. [DOI: 10.1016/j.lungcan.2020.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/12/2020] [Accepted: 07/14/2020] [Indexed: 12/25/2022]
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Woo HY, Na K, Yoo J, Chang JH, Park YN, Shim HS, Kim SH. Glioblastomas harboring gene fusions detected by next-generation sequencing. Brain Tumor Pathol 2020; 37:136-144. [PMID: 32761533 DOI: 10.1007/s10014-020-00377-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022]
Abstract
Oncogenic gene fusions have been reported in diffuse gliomas and may serve as potential therapeutic targets. Here, using next-generation sequencing analysis (Illumina TruSight Tumor 170 panel), we analyzed a total of 356 diffuse gliomas collected from 2017 to 2019 to evaluate clinical, pathological, and genetic features of gene fusion. We found 53 cases of glioblastomas harboring the following oncogenic gene fusions: MET (n = 18), EGFR (n = 14), FGFR (n = 12), NTRK (n = 5), RET (n = 2), AKT3 (n = 1), and PDGFRA fusions (n = 1). Gene fusions were consistently observed in both IDH-wildtype and IDH-mutant glioblastomas (8.8% and 9.4%, p = 1.000). PTPRZ1-MET fusion was the only fusion that genetically resembled secondary glioblastomas (i.e., high frequency of IDH mutation, ATRX loss, TP53 mutation, and absence of EGFR amplification), whereas other gene fusion types were similar to primary glioblastomas (i.e., high frequency of IDH-wildtype, TERT mutation, EGFR amplification, and PTEN mutation). In IDH-wildtype glioblastoma patients, multivariable analysis revealed that the PTPRZ1-MET fusion was associated with poor progression-free survival (HR [95% CI]: 5.42 (1.72-17.05), p = 0.004). Additionally, we described two novel cases of CCDC6-RET fusion in glioma. Collectively, our findings indicate that targetable gene fusions are associated with aggressive biological behavior and can aid the clinical treatment strategy for glioma patients.
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Affiliation(s)
- Ha Young Woo
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, 26 Kyungheedae-Ro, Dongdaemun-gu, Seoul, 02447, South Korea
| | - Jihwan Yoo
- Department of Neurosurgery, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Young Nyun Park
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea.
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Dong D, Shen G, Da Y, Zhou M, Yang G, Yuan M, Chen R. Successful Treatment of Patients with Refractory High-Grade Serous Ovarian Cancer with GOPC-ROS1 Fusion Using Crizotinib: A Case Report. Oncologist 2020; 25:e1720-e1724. [PMID: 32652753 DOI: 10.1634/theoncologist.2019-0609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recently, multiple poly (ADP-ribose) polymerase (PARP) inhibitors have demonstrated excellent efficacy among patients with ovarian cancer with or without BRCA mutations. However, alternative therapeutic options are urgently required for patients who cannot benefit from conventional chemotherapy or PARP inhibitors. CASE PRESENTATION A patient with high-grade serous ovarian carcinoma presented to our clinic after developing resistance to chemotherapy. Paired tumor-normal next-generation sequencing (NGS) was performed using peripheral blood to identify potential actionable mutations. NGS revealed the patient harboring a GOPC-ROS1 fusion, which was subsequently verified using a reverse transcription polymerase chain reaction assay. No germline or somatic mutation in BRCA1/2 or mismatch repair genes was detected. Therefore, the patient received crizotinib treatment. A rapid, favorable clinical response (partial response at 1 month) was observed, with further pathological response monitored and evaluated in follow-up interrogation. CONCLUSION This study suggested that crizotinib was an off-the-shelf, practical, and ostensibly effective treatment option for patients with ovarian cancer with ROS1 rearrangement. NGS-based genetic testing may guide to plan therapeutic paradigms, and render precision medicine promising in ovarian cancer treatment. IMPLICATIONS FOR PRACTICE Despite the previous report of ROS1 fusion in patients with ovarian cancer, it remains unknown whether patients can benefit from targeted therapeutic drugs. This study reports a GOPC-ROS1 fusion identified by next-generation sequencing in a patient with chemotherapy-resistant ovarian cancer. The patient was administered crizotinib and showed rapid, remarkable response. This study suggests that comprehensive sequencing should be offered for patients with ovarian cancer without effective therapeutic strategies, and crizotinib can be used to treat ROS1-rearranged ovarian carcinomas.
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Affiliation(s)
- Dapeng Dong
- Department of Oncology, Beijing Hui 'an Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, People's Republic of China
- Department of Oncology, Beijing Fengtai Youanmen Hospital, Beijing, People's Republic of China
| | - Ge Shen
- Department of Oncology, Beijing Hui 'an Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, People's Republic of China
- Department of Oncology, Beijing Fengtai Youanmen Hospital, Beijing, People's Republic of China
| | - Yong Da
- Department of Oncology, Beijing Hui 'an Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, People's Republic of China
- Department of Oncology, Beijing Fengtai Youanmen Hospital, Beijing, People's Republic of China
| | - Ming Zhou
- Department of Oncology, Beijing Hui 'an Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, People's Republic of China
- Department of Oncology, Beijing Fengtai Youanmen Hospital, Beijing, People's Republic of China
| | - Gang Yang
- Department of Oncology, Beijing Hui 'an Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, People's Republic of China
- Department of Oncology, Beijing Fengtai Youanmen Hospital, Beijing, People's Republic of China
| | - Mingming Yuan
- Geneplus-Beijing Ltd., Beijing, People's Republic of China
| | - Rongrong Chen
- Geneplus-Beijing Ltd., Beijing, People's Republic of China
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Clarke M, Mackay A, Ismer B, Pickles JC, Tatevossian RG, Newman S, Bale TA, Stoler I, Izquierdo E, Temelso S, Carvalho DM, Molinari V, Burford A, Howell L, Virasami A, Fairchild AR, Avery A, Chalker J, Kristiansen M, Haupfear K, Dalton JD, Orisme W, Wen J, Hubank M, Kurian KM, Rowe C, Maybury M, Crosier S, Knipstein J, Schüller U, Kordes U, Kram DE, Snuderl M, Bridges L, Martin AJ, Doey LJ, Al-Sarraj S, Chandler C, Zebian B, Cairns C, Natrajan R, Boult JKR, Robinson SP, Sill M, Dunkel IJ, Gilheeney SW, Rosenblum MK, Hughes D, Proszek PZ, Macdonald TJ, Preusser M, Haberler C, Slavc I, Packer R, Ng HK, Caspi S, Popović M, Faganel Kotnik B, Wood MD, Baird L, Davare MA, Solomon DA, Olsen TK, Brandal P, Farrell M, Cryan JB, Capra M, Karremann M, Schittenhelm J, Schuhmann MU, Ebinger M, Dinjens WNM, Kerl K, Hettmer S, Pietsch T, Andreiuolo F, Driever PH, Korshunov A, Hiddingh L, Worst BC, Sturm D, Zuckermann M, Witt O, Bloom T, Mitchell C, Miele E, Colafati GS, Diomedi-Camassei F, Bailey S, Moore AS, Hassall TEG, Lowis SP, Tsoli M, Cowley MJ, Ziegler DS, Karajannis MA, Aquilina K, Hargrave DR, Carceller F, Marshall LV, von Deimling A, Kramm CM, Pfister SM, Sahm F, Baker SJ, Mastronuzzi A, Carai A, Vinci M, Capper D, Popov S, Ellison DW, Jacques TS, Jones DTW, Jones C. Infant High-Grade Gliomas Comprise Multiple Subgroups Characterized by Novel Targetable Gene Fusions and Favorable Outcomes. Cancer Discov 2020; 10:942-963. [PMID: 32238360 PMCID: PMC8313225 DOI: 10.1158/2159-8290.cd-19-1030] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/03/2020] [Accepted: 03/20/2020] [Indexed: 11/16/2022]
Abstract
Infant high-grade gliomas appear clinically distinct from their counterparts in older children, indicating that histopathologic grading may not accurately reflect the biology of these tumors. We have collected 241 cases under 4 years of age, and carried out histologic review, methylation profiling, and custom panel, genome, or exome sequencing. After excluding tumors representing other established entities or subgroups, we identified 130 cases to be part of an "intrinsic" spectrum of disease specific to the infant population. These included those with targetable MAPK alterations, and a large proportion of remaining cases harboring gene fusions targeting ALK (n = 31), NTRK1/2/3 (n = 21), ROS1 (n = 9), and MET (n = 4) as their driving alterations, with evidence of efficacy of targeted agents in the clinic. These data strongly support the concept that infant gliomas require a change in diagnostic practice and management. SIGNIFICANCE: Infant high-grade gliomas in the cerebral hemispheres comprise novel subgroups, with a prevalence of ALK, NTRK1/2/3, ROS1, or MET gene fusions. Kinase fusion-positive tumors have better outcome and respond to targeted therapy clinically. Other subgroups have poor outcome, with fusion-negative cases possibly representing an epigenetically driven pluripotent stem cell phenotype.See related commentary by Szulzewsky and Cimino, p. 904.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Matthew Clarke
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Alan Mackay
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Britta Ismer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Jessica C Pickles
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ruth G Tatevossian
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tejus A Bale
- Department of Neuropathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Iris Stoler
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Elisa Izquierdo
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Sara Temelso
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Diana M Carvalho
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Valeria Molinari
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Anna Burford
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Louise Howell
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Alex Virasami
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Amy R Fairchild
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Aimee Avery
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jane Chalker
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Mark Kristiansen
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Kelly Haupfear
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - James D Dalton
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wilda Orisme
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ji Wen
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Hubank
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Kathreena M Kurian
- Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom
| | - Catherine Rowe
- Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom
| | - Mellissa Maybury
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Australia
- Oncology Service, Queensland Children's Hospital, Brisbane, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Stephen Crosier
- Newcastle Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Jeffrey Knipstein
- Division of Pediatric Hematology/Oncology/BMT, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ulrich Schüller
- Department of Neuropathology, University Hospital Hamburg-Eppendorf, and Research Institute Children's Cancer Center, Hamburg, Germany
- Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Kordes
- Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - David E Kram
- Section of Pediatric Hematology-Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Matija Snuderl
- Department of Neuropathology, NYU Langone Health, New York, New York
| | - Leslie Bridges
- Department of Neuropathology, St George's Hospital NHS Trust, London, United Kingdom
| | - Andrew J Martin
- Department of Neurosurgery, St George's Hospital NHS Trust, London, United Kingdom
| | - Lawrence J Doey
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, United Kingdom
| | - Safa Al-Sarraj
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, United Kingdom
| | - Christopher Chandler
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Bassel Zebian
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Claire Cairns
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Jessica K R Boult
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Simon P Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Martin Sill
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ira J Dunkel
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Stephen W Gilheeney
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marc K Rosenblum
- Department of Neuropathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Debbie Hughes
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Paula Z Proszek
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Tobey J Macdonald
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Matthias Preusser
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Roger Packer
- Center for Neuroscience and Behavioural Medicine, Children's National Medical Center, Washington, DC
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, China
| | - Shani Caspi
- Cancer Research Center, Sheba Medical Center, Tel Aviv, Israel
| | - Mara Popović
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Barbara Faganel Kotnik
- Department of Hematology and Oncology, University Children's Hospital, Ljubljana, Slovenia
| | - Matthew D Wood
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Lissa Baird
- Department of Neurosurgery, Oregon Health & Science University, Portland, Oregon
| | - Monika Ashok Davare
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, California
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Thale Kristin Olsen
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Petter Brandal
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Michael Farrell
- Department of Histopathology, Beaumont Hospital, Dublin, Ireland
| | - Jane B Cryan
- Department of Histopathology, Beaumont Hospital, Dublin, Ireland
| | - Michael Capra
- Paediatric Oncology, Our Lady's Children's Hospital, Dublin, Ireland
| | - Michael Karremann
- Department of Pediatrics, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jens Schittenhelm
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Germany
| | | | - Martin Ebinger
- Department of Pediatric Hematology and Oncology, University Hospital Tübingen, Germany
| | - Winand N M Dinjens
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Simone Hettmer
- Department of Pediatric Hematology and Oncology, University Hospital Freiburg, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Felipe Andreiuolo
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Pablo Hernáiz Driever
- Department of Paediatric Haematology/Oncology Charité Universitätsmedizin, Berlin, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Germany
| | - Lotte Hiddingh
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara C Worst
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dominik Sturm
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Zuckermann
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Tabitha Bloom
- BRAIN UK, University of Southampton, Southampton, United Kingdom
| | - Clare Mitchell
- BRAIN UK, University of Southampton, Southampton, United Kingdom
| | - Evelina Miele
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Giovanna Stefania Colafati
- Oncological Neuroradiology Unit, Department of Diagnostic Imaging, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | | | - Simon Bailey
- Newcastle Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Andrew S Moore
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Australia
- Oncology Service, Queensland Children's Hospital, Brisbane, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Timothy E G Hassall
- Oncology Service, Queensland Children's Hospital, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Stephen P Lowis
- Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom
| | - Maria Tsoli
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Mark J Cowley
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - David S Ziegler
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Kristian Aquilina
- Department of Neurosurgery, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Darren R Hargrave
- Department of Paediatric Oncology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Fernando Carceller
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Lynley V Marshall
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, University Medical Centre Göttingen, Germany
| | - Stefan M Pfister
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Department of Paediatric Haematology/Oncology Charité Universitätsmedizin, Berlin, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Suzanne J Baker
- Department of Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Angela Mastronuzzi
- Neuro-oncology Unit, Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Andrea Carai
- Oncological Neurosurgery Unit, Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - David Capper
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sergey Popov
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
- Department of Pathology, University of Wales Hospital NHS Trust, Cardiff, United Kingdom
| | - David W Ellison
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Thomas S Jacques
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom.
| | - David T W Jones
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom.
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Richardson TE, Tang K, Vasudevaraja V, Serrano J, William CM, Mirchia K, Pierson CR, Leonard JR, AbdelBaki MS, Schieffer KM, Cottrell CE, Tovar-Spinoza Z, Comito MA, Boué DR, Jour G, Snuderl M. GOPC-ROS1 Fusion Due to Microdeletion at 6q22 Is an Oncogenic Driver in a Subset of Pediatric Gliomas and Glioneuronal Tumors. J Neuropathol Exp Neurol 2020; 78:1089-1099. [PMID: 31626289 DOI: 10.1093/jnen/nlz093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ROS1 is a transmembrane receptor tyrosine kinase proto-oncogene that has been shown to have rearrangements with several genes in glioblastoma and other neoplasms, including intrachromosomal fusion with GOPC due to microdeletions at 6q22.1. ROS1 fusion events are important findings in these tumors, as they are potentially targetable alterations with newer tyrosine kinase inhibitors; however, whether these tumors represent a distinct entity remains unknown. In this report, we identify 3 cases of unusual pediatric glioma with GOPC-ROS1 fusion. We reviewed the clinical history, radiologic and histologic features, performed methylation analysis, whole genome copy number profiling, and next generation sequencing analysis for the detection of oncogenic mutation and fusion events to fully characterize the genetic and epigenetic alterations present in these tumors. Two of 3 tumors showed pilocytic features with focal expression of synaptophysin staining and variable high-grade histologic features; the third tumor aligned best with glioblastoma and showed no evidence of neuronal differentiation. Copy number profiling revealed chromosome 6q22 microdeletions corresponding to the GOPC-ROS1 fusion in all 3 cases and methylation profiling showed that the tumors did not cluster together as a single entity or within known methylation classes by t-Distributed Stochastic Neighbor Embedding.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | | | | | - Jonathan Serrano
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University
| | | | - Kanish Mirchia
- Department of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children's Hospital and The Ohio State University
| | | | | | - Mohamed S AbdelBaki
- Department of Pediatrics (MAC), State University of New York, Upstate Medical University, Syracuse, New York
| | - Kathleen M Schieffer
- Waters Center for Children's Cancer and Blood Disorders, State University of New York, Upstate Cancer Center, Syracuse, New York
| | - Catherine E Cottrell
- Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | | | - Melanie A Comito
- Department of Pathology, New York University Langone Health, New York, New York
| | - Daniel R Boué
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University
| | - George Jour
- Department of Neurological Surgery, Nationwide Children's Hospital
| | - Matija Snuderl
- Department of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children's Hospital and The Ohio State University
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Trevisan P, Graziadio C, Rodrigues DBK, Rosa RFM, Soares FP, Provenzi VO, de Oliveira CAV, Paskulin GA, Varella-Garcia M, Zen PRG. Clinical and Molecular Characterization of Adult Glioblastomas in Southern Brazil. J Neuropathol Exp Neurol 2020; 78:297-304. [PMID: 30840759 DOI: 10.1093/jnen/nlz006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We investigated 113 adult Brazilian patients with glioblastoma (GBM) for comparison with patients from distinct geographical areas and evaluation of suitability for novel targeted therapies. Patients were assessed for clinical features and tumor genomic characteristics such as ROS1 and NTRK1 rearrangements, KIT, PDGFRA, and KDR amplification, and RB1 deletion using multicolor fluorescence in situ hybridization. The majority of patients were male (53%), over 40 years (94%), with tumor located in single site (64%), in the right cerebral hemisphere (60%), and underwent partial resection (71%); 14% presented complications after surgery. The main clinical sign at diagnosis was focal abnormality (57%); frontal (31%); and temporal (20%) regions were most commonly affected. Median hospitalization time was 20 days, median survival was 175 days. One tumor was positive for rearrangement in NTRK1 and another in ROS1 (0.9% each). PDGFRA was amplified in 20% of cases, often co-amplified with KDR (>90%) and KIT (>60%). RB1 was deleted in 16% of patients. There was no association between these molecular abnormalities and patient survival. However, older age, complications after surgery, and right-sided tumors were independent variables associated with patient survival. This study contributes information on the molecular profile of glioblastomas in Latin America possibly supporting new target therapies.
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Affiliation(s)
| | - Carla Graziadio
- Clinical Genetics, Department of Internal Medicine, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Rafael Fabiano Machado Rosa
- Graduate Program in Pathology.,Clinical Genetics, Department of Internal Medicine, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiano Pasqualotto Soares
- Neurosurgery Section, Hospital Beneficência Portuguesa de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | | | | | - Paulo Ricardo Gazzola Zen
- Graduate Program in Pathology.,Clinical Genetics, Department of Internal Medicine, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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Reixachs-Solé M, Ruiz-Orera J, Albà MM, Eyras E. Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome. Nat Commun 2020; 11:1768. [PMID: 32286305 PMCID: PMC7156646 DOI: 10.1038/s41467-020-15634-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 03/11/2020] [Indexed: 12/14/2022] Open
Abstract
The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (ribosome profiling). We find evidence of translation for 40-50% of the expressed isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, and 33% in mouse. Differential splicing analysis revealed that about 40% of the splicing changes at RNA level are concordant with changes in translation. Furthermore, orthologous cassette exons between human and mouse preserve the directionality of the change, and are enriched in microexons in a comparison between glia and glioma. ORQAS leverages ribosome profiling to uncover a widespread and evolutionarily conserved impact of differential splicing on translation, particularly of microexon-containing isoforms.
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Affiliation(s)
- Marina Reixachs-Solé
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - M Mar Albà
- IMIM - Hospital del Mar Medical Research Institute, E08003, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, E08010, Barcelona, Spain
- Pompeu Fabra University, E08003, Barcelona, Spain
| | - Eduardo Eyras
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
- IMIM - Hospital del Mar Medical Research Institute, E08003, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies, E08010, Barcelona, Spain.
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41
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Brisudova A, Skarda J. Gene rearrangement detection by next-generation sequencing in patients with non-small cell lung carcinoma. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2020; 164:127-132. [PMID: 32284620 DOI: 10.5507/bp.2020.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/19/2020] [Indexed: 11/23/2022] Open
Abstract
Non-small cell lung carcinoma (NSCLC) is the leading cause of cancer-related deaths worldwide. Various molecular markers in NSCLC patients have been developed, including gene rearrangements, currently used in therapeutic strategies. With increasing number of these molecular biomarkers of NSCLC, there is a demand for highly efficient methods for detecting mutations and translocations in treatable targets. Those currently available U.S. Food and Drug Administration (FDA) approved approaches, for example imunohistochemisty (IHC) and fluorescence in situ hybridization (FISH), are inadequate, due to sufficient quantity of material and long time duration. Next-generation massive parallel sequencing (NGS), with the ability to perform and capture data from millions of sequencing reactions simultaneously could resolve the problem. Thanks to gradual NGS introduction into clinical laboratories, screening time should be considerably shorter, which is very important for patients with advanced NSCLC. Moreover, only a minimum sample input is needed for achieving adequate results. NGS was compared to the current detection methods of ALK, ROS1, c-RET and c-MET rearrangements in NSCLC and a significant match, between IHC, FISH and NGS results, was found. Recent available researches have been carried out on a small numbers of patients. Verifying these results on larger patients cohort is important. This review sumarizes the literature on this subject and compares current possibilities of predictive gene rearrangements detection in patients with NSCLC.
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Affiliation(s)
- Aneta Brisudova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Jozef Skarda
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
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42
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Abstract
Immunohistochemistry (IHC) is routinely performed in most laboratories, and other than purchase of commercially available antibodies, requires no additional equipment or reagents. As such, IHC is an accessible and relatively inexpensive test and one that can be performed quite quickly. This is in sharp contrast to genomic or mutational testing methodologies that are routinely "send out" tests as they require specialized equipment and reagents as well as individuals with expertise in the performance of the tests and analysis of the results, resulting in a prolonged turn-round-time and enhanced associated costs. However, many open questions remain in a rapidly changing therapeutic and scientific landscape with most obvious one being what exactly is the utility of "good old fashioned" IHC in the age of targeted therapy? For molecular applications, is a negative immunohistochemical result enough as a stand-alone diagnostic or predictive product? Is a positive immunohistochemical result perhaps more suitable for a role in screening for molecular alterations rather than a definitive testing modality? This review is an attempt to answer those very questions. We elucidate the broad range of entities in which IHC is currently used as a molecular surrogate and underscore pearls and pitfalls associated with each. Special attention is given to entities for which targeted therapies are currently available and to entities in which molecular data is of clinical utility as a prognosticator.
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Matjašič A, Zupan A, Boštjančič E, Pižem J, Popović M, Kolenc D. A novel PTPRZ1-ETV1 fusion in gliomas. Brain Pathol 2019; 30:226-234. [PMID: 31381204 DOI: 10.1111/bpa.12776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022] Open
Abstract
The aggressive nature of malignant gliomas and their genetic and clinical heterogeneity present a major challenge in their diagnosis and treatment. Development of targeted therapy brought attention on detecting novel gene fusions, since they represent promising therapeutic targets (eg, TRK inhibitors in NTRK fusion-positive tumors). Using targeted next-generation sequencing, we prospectively analyzed 205 primary brain tumors and detected a novel PTPRZ1-ETV1 fusion transcript in 11 of 191 (5.8%) gliomas, including nine glioblastomas, one anaplastic oligodendroglioma and one pilocytic astrocytoma. PTPRZ1-ETV1 fusion was confirmed by RT-PCR followed by Sanger sequencing, and in-silico analysis predicted a potential driver role. The newly detected fusion consists of the PTPRZ1 promoter in frame with the highly conserved DNA-binding domain of ETV1 transcription factor. The ETV1 and PTPRZ1 genes are known oncogenes, involved in processes of tumor development. ETV1 is a member of the ETS family of transcription factors, already known oncogenic drivers in Ewing sarcoma, prostate cancer and gastrointestinal stromal tumors, but not in gliomas. Its overexpression contributes to tumor growth and more aggressive tumor behavior. PTPRZ1 is already considered to be a tumor growth promoting oncogene in gliomas. In 8%-16% of gliomas, PTPRZ1 is fused to the MET oncogene, resulting in a PTPRZ1-MET fusion, which is associated with poorer prognosis but is also a positive predictive biomarker for treatment with kinase inhibitors. In view of the oncogenic role that the two fusion partners, PTPRZ1 and ETV1, exhibit in other malignancies, PTPRZ1-ETV1 fusion might present a novel potential therapeutic target in gliomas. Although histopathological examination of PTPRZ1-ETV1 fusion-positive gliomas did not reveal any specific or unique pathological features, and the follow-up period was too short to assess prognostic value of the fusion, careful monitoring of patients and their response to therapy might provide additional insights into the prognostic and predictive value of this novel fusion.
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Affiliation(s)
- Alenka Matjašič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jože Pižem
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mara Popović
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Danijela Kolenc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Targeting ROS1 Rearrangements in Non-small Cell Lung Cancer: Crizotinib and Newer Generation Tyrosine Kinase Inhibitors. Drugs 2019; 79:1277-1286. [DOI: 10.1007/s40265-019-01164-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ferguson SD, Zhou S, Huse JT, de Groot JF, Xiu J, Subramaniam DS, Mehta S, Gatalica Z, Swensen J, Sanai N, Spetzler D, Heimberger AB. Targetable Gene Fusions Associate With the IDH Wild-Type Astrocytic Lineage in Adult Gliomas. J Neuropathol Exp Neurol 2019; 77:437-442. [PMID: 29718398 PMCID: PMC5961205 DOI: 10.1093/jnen/nly022] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gene fusions involving oncogenes have been reported in gliomas and may serve as novel therapeutic targets. Using RNA-sequencing, we interrogated a large cohort of gliomas to assess for the incidence of targetable genetic fusions. Gliomas (n = 390) were profiled using the ArcherDx FusionPlex Assay. Fifty-two gene targets were analyzed and fusions with preserved kinase domains were investigated. Overall, 36 gliomas (9%) harbored a total of 37 potentially targetable fusions, the majority of which were found in astrocytomas (n = 34). Within this lineage 11% (25/235) of glioblastomas, 12% (5/42) of anaplastic astrocytomas, 8% (2/25) of grade II astrocytomas, and 33% (2/6) of pilocytic astrocytoma harbored targetable fusions. Fusions were significantly more frequent in IDH wild-type tumors (12%, n = 31/261) relative to IDH mutants (4%; n = 4/109) (p = 0.011). No fusions were seen in oligodendrogliomas. The most frequently observed therapeutically targetable fusions were in FGFR (n = 12), MET (n = 11), and NTRK (n = 8). Several additional novel fusions that have not been previously described in gliomas were identified including EGFR:VWC2 and FGFR3:NBR1. In summary, targetable gene fusions are enriched in IDH wild-type high-grade astrocytic tumors, which will influence enrollment in and interpretation of clinical trials of glioma patients.
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Affiliation(s)
- Sherise D Ferguson
- Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shouhao Zhou
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason T Huse
- Department of Neuropathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John F de Groot
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Deepa S Subramaniam
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Shwetal Mehta
- Barrow Neurological Institute and Barrow Neurosurgical Associates, Phoenix, Arizona
| | | | | | - Nader Sanai
- Barrow Neurological Institute and Barrow Neurosurgical Associates, Phoenix, Arizona
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Ou SHI, Zhu VW. CNS metastasis in ROS1+ NSCLC: An urgent call to action, to understand, and to overcome. Lung Cancer 2019; 130:201-207. [DOI: 10.1016/j.lungcan.2019.02.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/11/2019] [Accepted: 02/21/2019] [Indexed: 01/14/2023]
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Marks EI, Pamarthy S, Dizon D, Birnbaum A, Yakirevich E, Safran H, Carneiro BA. ROS1-GOPC/FIG: a novel gene fusion in hepatic angiosarcoma. Oncotarget 2019; 10:245-251. [PMID: 30719217 PMCID: PMC6349438 DOI: 10.18632/oncotarget.26521] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatic angiosarcoma (HAS) is a rare and highly lethal malignancy with few effective systemic treatments. Relatively little is known about the genetic abnormalities that drive this disease. As a result, there has been minimal progress towards applying targeted therapies to the treatment of HAS. We describe the first reported case of a patient with HAS that harbored a fusion of ROS1 with GOPC/FIG. Similar to other rearrangements involving ROS1, the resulting fusion protein is believed to act as a major driver of carcinogenesis and may be subject to inhibition by drugs that target ROS1 such as crizotinib. We then queried the MSK-IMPACT clinical sequencing cohort and cBioportal datasets, demonstrating the previously unknown prevalence of ROS1-GOPC fusions in soft tissue sarcomas and hepatobiliary cancers. Amplification of these genes was also found to correlate with reduced overall survival. This is followed by a review of the role played by ROS1 rearrangements in cancer, as well as the evidence supporting the use of targeted therapies against the resulting fusion protein. We suggest that testing for ROS1 fusion and, if positive, treatment with a targeted therapy could be considered at the time of diagnosis for patients with angiosarcoma. This report also highlights the need for further investigation into the molecular pathophysiology of this deadly disease.
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Affiliation(s)
- Eric I. Marks
- Division of Hematology-Oncology, Lifespan Cancer Institute, Warren-Alpert Medical School of Brown University, Providence, RI, USA
| | - Sahithi Pamarthy
- Atrin Pharmaceuticals, Pennsylvania Biotechnology Center, Doylestown, PA, USA
| | - Don Dizon
- Division of Hematology-Oncology, Lifespan Cancer Institute, Warren-Alpert Medical School of Brown University, Providence, RI, USA
| | - Ari Birnbaum
- Division of Hematology-Oncology, Lifespan Cancer Institute, Warren-Alpert Medical School of Brown University, Providence, RI, USA
| | - Evgeny Yakirevich
- Department of Pathology, Lifespan Cancer Institute, Warren-Alpert Medical School of Brown University, Providence, RI, USA
| | - Howard Safran
- Division of Hematology-Oncology, Lifespan Cancer Institute, Warren-Alpert Medical School of Brown University, Providence, RI, USA
| | - Benedito A. Carneiro
- Division of Hematology-Oncology, Lifespan Cancer Institute, Warren-Alpert Medical School of Brown University, Providence, RI, USA
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48
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Majerska J, Feretzaki M, Glousker G, Lingner J. Transformation-induced stress at telomeres is counteracted through changes in the telomeric proteome including SAMHD1. Life Sci Alliance 2018; 1:e201800121. [PMID: 30456372 PMCID: PMC6238619 DOI: 10.26508/lsa.201800121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
The authors apply telomeric chromatin analysis to identify factors that accumulate at telomeres during cellular transformation, promoting telomere replication and repair and counteracting oncogene-borne telomere replication stress. Telomeres play crucial roles during tumorigenesis, inducing cellular senescence upon telomere shortening and extensive chromosome instability during telomere crisis. However, it has not been investigated if and how cellular transformation and oncogenic stress alter telomeric chromatin composition and function. Here, we transform human fibroblasts by consecutive transduction with vectors expressing hTERT, the SV40 early region, and activated H-RasV12. Pairwise comparisons of the telomeric proteome during different stages of transformation reveal up-regulation of proteins involved in chromatin remodeling, DNA repair, and replication at chromosome ends. Depletion of several of these proteins induces telomere fragility, indicating their roles in replication of telomeric DNA. Depletion of SAMHD1, which has reported roles in DNA resection and homology-directed repair, leads to telomere breakage events in cells deprived of the shelterin component TRF1. Thus, our analysis identifies factors, which accumulate at telomeres during cellular transformation to promote telomere replication and repair, resisting oncogene-borne telomere replication stress.
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Affiliation(s)
- Jana Majerska
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marianna Feretzaki
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Galina Glousker
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Pacenta HL, Macy ME. Entrectinib and other ALK/TRK inhibitors for the treatment of neuroblastoma. DRUG DESIGN DEVELOPMENT AND THERAPY 2018; 12:3549-3561. [PMID: 30425456 PMCID: PMC6204873 DOI: 10.2147/dddt.s147384] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RTK plays important roles in many cellular signaling processes involved in cancer growth and development. ALK, TRKA, TRKB, TRKC, and ROS1 are RTKs involved in several canonical pathways related to oncogenesis. These proteins can be genetically altered in malignancies, leading to receptor activation and constitutive signaling through their respective downstream pathways. Neuroblastoma (NB) is the most common extracranial solid tumor in childhood, and despite intensive therapy, there is a high mortality rate in cases with a high-risk disease. Alterations of ALK and differential expression of TRK proteins are reported in a proportion of NB. Several inhibitors of ALK or TRKA/B/C have been evaluated both preclinically and clinically in the treatment of NB. These agents have had variable success and are not routinely used in the treatment of NB. Entrectinib (RXDX-101) is a pan-ALK, TRKA, TRKB, TRKC, and ROS1 inhibitor with activity against tumors with ALK, NTRK1, NTRK2, NTRK3, and ROS1 alterations in Phase I clinical trials in adults. Entrectinib’s activity against both ALK and TRK proteins suggests a possible role in NB treatment, and it is currently under investigation in both pediatric and adult oncology patients.
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Affiliation(s)
- Holly L Pacenta
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, Aurora, CO, USA,
| | - Margaret E Macy
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, Aurora, CO, USA,
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50
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Davare MA, Henderson JJ, Agarwal A, Wagner JP, Iyer SR, Shah N, Woltjer R, Somwar R, Gilheeney SW, DeCarvalo A, Mikkelson T, Van Meir EG, Ladanyi M, Druker BJ. Rare but Recurrent ROS1 Fusions Resulting From Chromosome 6q22 Microdeletions are Targetable Oncogenes in Glioma. Clin Cancer Res 2018; 24:6471-6482. [PMID: 30171048 DOI: 10.1158/1078-0432.ccr-18-1052] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/25/2018] [Accepted: 08/28/2018] [Indexed: 02/03/2023]
Abstract
PURPOSE Gliomas, a genetically heterogeneous group of primary central nervous system tumors, continue to pose a significant clinical challenge. Discovery of chromosomal rearrangements involving kinase genes has enabled precision therapy, and improved outcomes in several malignancies. EXPERIMENTAL DESIGN Positing that similar benefit could be accomplished for patients with brain cancer, we evaluated The Cancer Genome Atlas (TCGA) glioblastoma dataset. Functional validation of the oncogenic potential and inhibitory sensitivity of discovered ROS1 fusions was performed using three independent cell-based model systems, and an in vivo murine xenograft study. RESULTS In silico analysis revealed previously unreported intrachromosomal 6q22 microdeletions that generate ROS1-fusions from TCGA glioblastoma dataset. ROS1 fusions in primary glioma and ependymoma were independently corroborated from MSK-IMPACT and Foundation Medicine clinical datasets. GOPC-ROS1 is a recurrent ROS1 fusion in primary central nervous system (CNS) tumors. CEP85L-ROS1 and GOPC-ROS1 are transforming oncogenes in cells of astrocytic lineage, and amenable to pharmacologic inhibition with several ROS1 inhibitors even when occurring concurrently with other cancer hotspot aberrations frequently associated with glioblastoma. Oral monotherapy with a brain-permeable ROS1 inhibitor, lorlatinib, significantly prolonged survival in an intracranially xenografted tumor model generated from a ROS1 fusion-positive glioblastoma cell line. CONCLUSIONS Our findings highlight that CNS tumors should be specifically interrogated for these rare intrachromosomal 6q22 microdeletion events that generate actionable ROS1 fusions. ROS1 fusions in primary brain cancer may be amenable for clinical intervention with kinase inhibitors, and this holds the potential of novel treatment paradigms in these treatment-refractory cancer types, particularly in glioblastoma.
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Affiliation(s)
- Monika A Davare
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Pediatric Research Institute, Oregon Health and Sciences University, Portland, Oregon.
| | - Jacob J Henderson
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Pediatric Research Institute, Oregon Health and Sciences University, Portland, Oregon
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon
| | - Jacob P Wagner
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon
| | - Sudarshan R Iyer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Pediatric Research Institute, Oregon Health and Sciences University, Portland, Oregon
| | - Nameeta Shah
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle Washington
| | - Randy Woltjer
- Department of Pathology, Oregon Health and Sciences University, Portland, Oregon
| | - Romel Somwar
- Department of Pathology, Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen W Gilheeney
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, Michigan
| | - Ana DeCarvalo
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tom Mikkelson
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Erwin G Van Meir
- Departments of Neurosurgery and Hematology & Medical Oncology, School of Medicine and Winship Cancer Institute Emory University, Atlanta, Georgia
| | - Marc Ladanyi
- Department of Pathology, Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon.,Howard Hughes Medical Institute, Portland, Oregon
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